Journal Article

Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x

Vincent J. Carey, Adam R. Davis, Michael F. Lawrence, Robert Gentleman and Benjamin A. Raby

in Bioinformatics

Volume 25, issue 11, pages 1447-1448
Published in print June 2009 | ISSN: 1367-4803
Published online April 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp169
Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x

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Summary: Associations between DNA polymorphisms and mRNA abundance are a natural target of genetic investigations, and microarrays facilitate genome-wide and transcriptome-wide surveys of these associations. This work is motivated by emerging requirements for data architectures and algorithm interfaces to allow flexible exploration of public and private archives of genotyping and expression arrays. Using R/Bioconductor facilities, Phase II HapMap genotypes and Illumina 47K expression assay results archived on multiple populations may be interactively explored and analyzed using commodity hardware.

Availability and Implementation: Open Source. Bioconductor 2.3 packages GGtools, GGBase, GGdata, hmyriB36. Freely available on the web at http://www.bioconductor.org

Contact: stvjc@channing.harvard.edu

Journal Article.  963 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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